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reactome
logic-network-generator
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Regulator wiring: set-pool nodes (default on), cap pools (off), drugs.csv
- #99
#99
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adamjohnwright
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Sep 28, 2026
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Regulator wiring: set-pool nodes (default on), cap pools (off), drugs.csv
#99
adamjohnwright
merged 9 commits into
main
reactome/logic-network-generator:main
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feat/set-pool
reactome/logic-network-generator:feat/set-pool
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drugs.csv: ship the pathway's drug-derived entities (Drug; complex with any drug component; set whose every member is one) beside cofactors.csv, for a consumer modelling a cell without the drug (de…
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Review of #98: drugs.csv in its own try block after containment (a failed drug query no longer costs containment.csv); class+name from the structure query (the unlabelled MATCH scanned every node, …
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Commits on Sep 27, 2026
LNG_SET_POOL (deltasignal specs/033, default off): a bare EntitySet catalyst/regulator becomes one pool node (the set) fed by set_member edges, feeding each reaction copy once, instead of every mem…
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Review of set-pool: a pooled catalyst no longer depletes its own member (the stId guards compared the SET's id; 4 E3-ligase sets would have closed member->pool-|member cycles); pooling only under c…
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LNG_SET_POOL default on (trial, specs/033: held-out +6, tuning +10, exp +3); legacy regulator tests pinned to LNG_SET_POOL=0; test that pooling is the default
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WIP LNG_CAP_POOLS (deltasignal specs/036, default off): a set input that resolves to several nodes in one virtual reaction (alternatives bundled by the variant cap) is emitted as a set pool feeding…
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tests for LNG_CAP_POOLS: bundled alternatives pooled, single chosen member not, flag off, no leak between pathways, modifier sets excluded
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Merge remote-tracking branch 'origin/feat/drugs-csv' into feat/combined-037
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Review of combined-037: cap pools only in reactions the variant cap bundled (CAPPED_IDS; an uncapped copy's chosen complex alternative resolves to co-required subunits -- miR-93 RISC in PIP3 was av…
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